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Release candidate microSALT 4.1.0#195

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Merged

karlnyr merged 49 commits intomasterClinical-Genomics/microSALT:masterfrom rc410Clinical-Genomics/microSALT:rc410Copy head branch name to clipboardJan 8, 2025

+1,037-772

Commits

Commits on Dec 6, 2024

• PubMLST authentication utilities

  ahdamin

  committed
  45ff7d7

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• Refactor PubMLST data fetching

  ahdamin

  committed
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Commits on Dec 7, 2024

• Add quotations

  ahdamin

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Commits on Dec 9, 2024

• Add rauth v0.7.3

  ahdamin

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Commits on Dec 11, 2024

• Add pubmlst config

  ahdamin

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• Add pubmlst config loader

  ahdamin

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• Add session token validation

  ahdamin

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• Improve OAuth credentials usage

  ahdamin

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• Read credentials from config

  ahdamin

  committed
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• dd OAuth header generation

  ahdamin

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  1c0c62c

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• Refactor PubMLST fetch process

  ahdamin

  committed
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Commits on Dec 12, 2024

• Update database query checks

  ahdamin

  committed
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• Add logger to authentication

  ahdamin

  committed
  b98b2d3

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• Handle nested db entries and kip non-sequence dbs

  ahdamin

  committed
  882d0c8

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• Remove credentials file

  ahdamin

  committed
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• Replace print with logger

  ahdamin

  committed
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• Add reusable path resolver

  ahdamin

  committed
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• Enhance logging for Auth

  ahdamin

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• Match organisms

  ahdamin

  committed
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Commits on Dec 13, 2024

• Handle MLST profiles in CSV format

  ahdamin

  committed
  f1de77f

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• Add PubMLST congis and improve config path checks

  ahdamin

  committed
  817bd90

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• Improve config path handling

  ahdamin

  committed
  826bfec

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• Replace f-strings with format

  ahdamin

  committed
  95c4ba2

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• Refactor path handling functions

  ahdamin

  committed
  d01cc5a

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• Improve exception handling

  ahdamin

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  5e129f9

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• Ensure directories exist

  ahdamin

  committed
  f8c8c04

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• Add check_database_metadata

  ahdamin

  committed
  2b87fca

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• Fix methods position

  ahdamin

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  1235c6a

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• Fix logger

  ahdamin

  committed
  f70e836

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Commits on Dec 16, 2024

• Add client, constants, and exceptions

  ahdamin

  committed
  8268a3f

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• Fix checks for pubmlst config

  ahdamin

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Commits on Dec 17, 2024

• Add URL rules for pubmlst db

  ahdamin

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• Add InvalidURLError

  ahdamin

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  d7a7c92

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• Add URL parsing helper

  ahdamin

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• Add MLST scheme retrieval & URL parsing helper

  ahdamin

  committed
  a5f4c71

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• Replace manual HTTP requests with PubMLSTClient

  ahdamin

  committed
  977a240

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• Remove client object

  ahdamin

  committed
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• Fix tests

  Vince-janv

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Commits on Dec 18, 2024

• Add pubmlst utils (#188)

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  ahdamin

  and

  Vince-janv

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Commits on Jan 7, 2025

• Merge pull request #189 from Clinical-Genomics/rc410 (minor)

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  karlnyr

  authored
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• Revert "Release candidate v4.1.0"

  karlnyr

  authored
  32e9494

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• bump version

  karlnyr

  committed
  547a4fe

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• Merge pull request #190 from Clinical-Genomics/revert-189-rc410

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  karlnyr

  authored
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• Merge branch 'master' into rc410

  karlnyr

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• Merge pull request #191 from Clinical-Genomics/rc410

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  karlnyr

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Commits on Jan 8, 2025

• Merge branch 'master' into add-pubmlst-utils

  karlnyr

  authored
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• Merge pull request #192 from Clinical-Genomics/add-pubmlst-utils (patch)

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  karlnyr

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• Merge pull request #194 from Clinical-Genomics/add-pubmlst-utils

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  karlnyr

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• Merge branch 'master' into rc410

  karlnyr

  committed
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